A near complete, chromosome-scale assembly of the black raspberry (<i>Rubus occidentalis</i>) genome

VanBuren, Robert; Wai, Ching Man; Colle, Marivi; Wang, Jie; Sullivan, Shawn; Bushakra, Jill M.; Liachko, Ivan; Vining, Kelly J.; Dossett, Michael; Finn, Chad E.; Jibran, Rubina; Chagné, David; Childs, Kevin L.; Edger, Patrick P.; Mockler, Todd C.; Bassil, Nahla V.

doi:10.1093/gigascience/giy094

Cited by 94 publications

(89 citation statements)

References 33 publications

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“…In this study, we used deep PacBio sequencing and Hi-C linkage information to overcome the repetitive regions and achieve better assembly characteristics. The combination of longread and linkage data are a powerful toolset to produce chromosome-level assemblies, which are currently being increasingly used in a large number of species (e.g., Gordon et al 2016;Gong et al 2018;VanBuren et al 2018;Low et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Chromosome-Level Assembly of theCaenorhabditis remaneiGenome Reveals Conserved Patterns of Nematode Genome Organization

2020

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The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of interchromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species.

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Section: Discussionmentioning

confidence: 99%

Chromosome-Level Assembly of theCaenorhabditis remaneiGenome Reveals Conserved Patterns of Nematode Genome Organization

2020

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“…In addition, we also analysed syntenic positions in Rubus occidentalis, a species from the Rosoideae sub-family, for which a chromosome scale assembly recently became available [27]. Synteny analysis of the genes surrounding the TNL clusters revealed no Rdr1 homologs in syntenic positions for P. persica, M. x domestica and R. occidentalis (S1 Table).…”

Section: Tnl Structure In Other Rosaceaementioning

confidence: 99%

Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily

et al. 2020

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The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis 'Old Blush' genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70-80 million years ago during the Cretaceous period.

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“…Hi‐C, a new technology providing contact frequencies between sequences, has revolutionized the assembly to chromosomes. For plants it was notably applied to the 5 Gb barley and 12 Gb wild emmer genome (Avni et al ., ; Mascher et al ., ) and has allowed chromosome‐scale assemblies without a genetic map for example for raspberry (Van Buren et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Computational aspects underlying genome to phenome analysis in plants

et al. 2019

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Summary Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high‐throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait−trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.

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A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

Cited by 94 publications

References 33 publications

Chromosome-Level Assembly of theCaenorhabditis remaneiGenome Reveals Conserved Patterns of Nematode Genome Organization

Chromosome-Level Assembly of theCaenorhabditis remaneiGenome Reveals Conserved Patterns of Nematode Genome Organization

Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily

Computational aspects underlying genome to phenome analysis in plants

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